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Recently, analysis of facial morphology and its relationship to genes has received considerable attention. In this paper, we present a scheme of 3D shape alignment for the morphological study of human face. We employ the Cylindrical Polar transform to sample the original 3D shape data which was obtained using the 3D laser scanner. By mapping the sampled data to a 2D image, we can obtain the shape feature points manually, then these feature points are mapped back to 3D coordinate and are used to 3D shape alignment based on Generalized Procrustes Analysis (GPA). The experimental results show the effectiveness of the proposed method for 3D shape alignment.